Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards
☆47Sep 29, 2021Updated 5 years ago
Alternatives and similar repositories for benchmarksets
Users that are interested in benchmarksets are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆16Dec 24, 2016Updated 9 years ago
- Benchmark set for relative free energy calculations.☆123May 22, 2024Updated 2 years ago
- An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.☆203Jul 6, 2023Updated 3 years ago
- Set up relative free energy calculations using a common scaffold☆25Apr 21, 2026Updated 6 months ago
- Templates for use in preparing articles for the Living Journal of Computational Molecular Sciences (LiveCoMS)☆11Jul 20, 2026Updated 3 months ago
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- ☆25Oct 30, 2020Updated 6 years ago
- Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…☆19Oct 27, 2022Updated 4 years ago
- This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration fr…☆34Jun 3, 2025Updated last year
- Tautomer ratios in solution☆28Sep 20, 2021Updated 5 years ago
- A tool for setting up free energy simulations.☆37Oct 20, 2022Updated 4 years ago
- Python implementation of the multistate Bennett acceptance ratio (MBAR)☆319Feb 12, 2026Updated 8 months ago
- Alchemical mutation scoring map☆42Apr 7, 2022Updated 4 years ago
- Probabilistic Inference for NOvel Therapeutics☆15Feb 5, 2022Updated 4 years ago
- Advanced toolkit for binding free energy calculations☆36Sep 2, 2025Updated last year
- End-to-end encrypted email - Proton Mail • AdSpecial offer: 40% Off Yearly / 80% Off First Month. All Proton services are open source and independently audited for security.
- BLaDE is a Basic Lambda Dynamics Engine for molecular dynamics based alchemical free energy calculations using multisite lambda dynamics …☆20Oct 23, 2026Updated last week
- Automated omics-scale protein modeling and simulation setup.☆53Sep 20, 2021Updated 5 years ago
- Dihedral scanner with wavefront propagation☆38May 3, 2025Updated last year
- A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD☆17Apr 3, 2026Updated 6 months ago
- Bayesian tools for fitting molecular mechanics torsion parameters to quantum chemical data.☆21Sep 20, 2021Updated 5 years ago
- Software tools for fragment-based drug discovery (FBDD)☆27Apr 6, 2020Updated 6 years ago
- Bayesian Multistate Bennett Acceptance Ratio Method☆16Oct 16, 2026Updated 2 weeks ago
- Differentiate all the things!☆178Jan 9, 2026Updated 9 months ago
- ☆10Feb 18, 2020Updated 6 years ago
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- A primer on software development best practices for computational chemistry☆279Dec 5, 2022Updated 3 years ago
- Package for consistent reporting of relative free energy results☆43Oct 23, 2026Updated last week
- Sire Molecular Simulations Framework☆98Jul 17, 2023Updated 3 years ago
- ☆29Dec 1, 2020Updated 5 years ago
- Experiments with expanded ensembles to explore chemical space☆204Oct 28, 2025Updated last year
- the simple alchemistry library☆248Jun 1, 2026Updated 4 months ago
- Parameter/topology editor and molecular simulator☆457Oct 21, 2026Updated last week
- ☆77Aug 13, 2026Updated 2 months ago
- ☆49Feb 17, 2026Updated 8 months ago
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- A document for the Living Journal of Computational Molecular Science (LiveCoMS) which describes basic training for molecular simulations …☆119Dec 29, 2018Updated 7 years ago
- A fast solver for large scale MBAR/UWHAM equations☆42Sep 4, 2024Updated 2 years ago
- Cloud GPU supported NAMD3-based binding free energy difference between two small molecules against the same protein target. This is prob…☆28Oct 21, 2026Updated last week
- Soft benchmark sets for alchemical free energy calculations, for assessing their accuracy on biomolecular systems☆18Mar 8, 2019Updated 7 years ago
- An automated framework for generating optimized partial charges for molecules☆40Updated this week
- An implementation of the Free-Wilson SAR analysis method using the RDKit☆67Sep 5, 2022Updated 4 years ago
- Extract ligand binding sites from PDB. Match the binding sites to de novo scaffolds.☆13Dec 29, 2020Updated 5 years ago